Download Bioinformatics: Origins, Definitions, and Techniques in Genomics - Prof. Roman E. Boldyref and more Study notes Biology in PDF only on Docsity! Bioinformatics 1. Origins 2. Definitions 3. Gene Expression Data 4. Comparative Genomics 5. Structural & Functional Genomics Bioinformatics Origins 1. Large amounts of data from high throughput experiments, entire genome sequences, and measuring gene expression of entire genome 2. Lab & note books impractical to store, analyze, & display gene sequence & expression data 3. Polymer nature of DNA, RNA, & proteins favor mathematical analysis Gene Expression Data 1. Compares expression of several genes in response to single environmental factor, example gradual O2 loss 2. Looks at each gene’s expression over time & for gene’s with similar expression patterns 3. Fold change & log transformation 4. Correlation Coefficient, r Fold Change & Log Transformation 1. Ratio of experimental to control expression levels 2. Log2 or log10 of ratios compared in table gene 0hr 2hr 4hr 6hr 8hr 10hr a 0 1.00 1.58 2.00 1.58 1.00 b 0 -1.00 -1.60 -2.00 -1.60 -1.00 c 0 1.00 1.58 2.00 1.58 1.00 Correlation coefficient, r 1. Values of 1 indicate perfect agreement 2. Values of -1 indicate expression of one gene represses another gene 3. Gene clusters Comparative Genomics 1. Differences and similarities between all genes of multiple species 2. Species clustered in dendrogram 3. Species relatedness or not 4. Evolutionary relationships Phylogenetic Dendrograms
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b. Other possibilities
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Structural & Functional Genomics 1. Structural- attempts to crystallize and/or predict the structures of all proteins in organism 2. Functional- identifies gene functions and associations of genes Large Subunit 1. Two strands, one long & one short 2. Long strand functions as ribozyme 3. Enzyme-like activity that helps form peptide bond between amino acids Small Subunit 1. Medium length RNA strand 2. Functional part of ribosome 3. Lines up tRNA anticodon with its complementary mRNA codon 4. Allows other end of tRNA & its amino acid to interact with ribozyme of large subunit 16s rRNA gene 1. Gene for small subunit RNA strand, strongly conserved 2. Woese, 1970, first used rRNA to demonstrate differences between bacteria & archeae 3. Standard is all phylogenetic studies 4. Comparing 16s sequences can measure how long since two species have diverged
